The Kim Nirvana was carrying 189 people Thursday when officials said it went down only a kilometer from Ormoc City on the island of Leyte.
The coast guard said at least 127 people have been rescued. Divers are searching the partially submerged vessel for at least 26 others who remain missing.
Officials are investigating whether bad weather or human error led to the wreck of the wooden ship, which had just embarked on its regular route to the Camotes Islands.
Ferry accidents kill dozens, if not hundreds, of people each year in the Philippines, thanks in part to overcrowding and poor safety standards.
Passenger boats are an important mode of transportation in the archipelago nation, which is made up of more than 7,000 islands.